measuring morphological diversity and tempo using discrete characters: advantages and disadvantages...

Measuring morphological diversity and tempo using discrete characters: advantages and disadvantages of

including additional phylogenetic information

Graeme T. Lloyd @GraemeTLloyd

Acknowledgements

Emma SherrattThomas Guillerme

Discrete morphology

Discrete morphology

Discrete morphology

?

Discrete morphology

Discrete morphology

Discrete morphology

github.com/graemetlloyd/Claddis

Claddis

Lloyd 2016

github.com/graemetlloyd/Claddis

Claddis

Lloyd 2016

github.com/graemetlloyd/Claddis

Claddis

Lloyd 2016

github.com/graemetlloyd/Claddis

Claddis

Lloyd 2016

STR

github.com/graemetlloyd/Claddis

Claddis

Lloyd 2016

STR

#NEXUS

TNT/Hennig86

Claddis

Claddis

?

Claddis

(01)?

Claddis

(01)

0 1 2

1

1

?

Claddis

(01)

0 1 2

1

1

?

Outline

Phylogeny and disparity

Phylogeny and disparity

Increase sample size

Brusatte et al 2011

Phylogeny and disparity

Increase sample size Estimate missing states

Brusatte et al 2011; Butler et al 2011

Phylogeny and disparity

Increase sample size Estimate missing states

Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015

Create phylomorphospace

Two phylomorphospace types

Two phylomorphospace types

Two phylomorphospace types

Brusatte et al 2011; Butler et al 2011

Two phylomorphospace types

Brusatte et al 2011; Butler et al 2011

Two phylomorphospace types

Brusatte et al 2011; Butler et al 2011; Hopkins and Smith 2015

Two phylomorphospace types

Two phylomorphospace types

Estim

ate

tip st

ates

Estimate all ancestral statesN Y

NY

Two phylomorphospace types

Estim

ate

tip st

ates

Estimate all ancestral statesN Y

NY

Two phylomorphospace types

Estim

ate

tip st

ates

Estimate all ancestral statesN Y

NY

Questions

Questions

How do phylomorphospace choices affect our inferences?To what degree are we measuring phylogenetic rather than

morphological signal?

Questions

How do phylomorphospace choices affect our inferences?To what degree are we measuring phylogenetic rather than

morphological signal?

Disparity dataset

152 taxa | 853 characters

Disparity dataset

Results: layout

N Y

NY

N Y

NY

N Y

NY

N Y

NY

Results: scree plots

Lloyd in prep

Results: visualisation

Lloyd in prep

r = 0.188

r = 0.204

r = 0.354

r = 0.653

r = 0.396

r = 0.841

Results: phylogenetic correlation

Lloyd in prep

Results: root distance

Lloyd in prep

Results: root distance rate

Lloyd in prep

Rate equations

Rate equations

𝑅𝑎𝑡𝑒=h𝐶 𝑎𝑛𝑔𝑒𝑇𝑖𝑚𝑒

Rate equations

𝑅𝑎𝑡𝑒=h𝐶 𝑎𝑛𝑔𝑒𝑇𝑖𝑚𝑒

𝑅𝑎𝑡𝑒=h𝐶 𝑎𝑛𝑔𝑒

𝑇𝑖𝑚𝑒×𝐶𝑜𝑚𝑝𝑙𝑒𝑡𝑒𝑛𝑒𝑠𝑠

Rate questions

Rate questions

Rate questions

Rate questions

Rate questions

Rate questions

Rate questions

Time

Rate questions

Time Change

Rate questions

Time Change

Completeness

Rate time series

Rate time series

Ruta et al 2006

Branches binned(Time)

Rate time series

Ruta et al 2006; Lloyd et al 2012

Stochastic changes(Change)

Branches binned(Time)

Rate time series

Ruta et al 2006; Lloyd et al 2012; Close et al 2015

Stochastic changes(Change)

Branches binned(Time)

Weighted average(Completeness)

Questions

Questions

How does ASR choice affect rate time series?How does correcting for completeness affect rate time series?

Questions

How does ASR choice affect rate time series?How does correcting for completeness affect rate time series?

Rate dataset

86 taxa | 91 characters

Rate dataset

Westoll 1949

Rate results

Rate resultsACCTRAN DELTRAN Likelihood Likelihood

+ Corr. 1Likelihood+ Corr. 2

Rate resultsACCTRAN DELTRAN Likelihood Likelihood

+ Corr. 1Likelihood+ Corr. 2

Lloydet al2012

Lloydet al2012

Brusatteet al2014

Closeet al2015

Lloyd2016

Rate resultsACCTRAN DELTRAN Likelihood Likelihood

+ Corr. 1Likelihood+ Corr. 2

Lloydet al2012

Lloydet al2012

Brusatteet al2014

Closeet al2015

Lloyd2016

Rate resultsACCTRAN DELTRAN Likelihood Likelihood

+ Corr. 1Likelihood+ Corr. 2

Lloydet al2012

Lloydet al2012

Brusatteet al2014

Closeet al2015

Lloyd2016

Rate resultsACCTRAN DELTRAN Likelihood Likelihood

+ Corr. 1Likelihood+ Corr. 2

1.39 1.77 0.78 0.23 0.78

Lloydet al2012

Lloydet al2012

Brusatteet al2014

Closeet al2015

Lloyd2016

Wobble index:

Conclusions

Conclusions

Conclusions

Conclusions

1.77

0.78

Conclusions

1.77

0.78